From ae8b3d27ea11b708253bfd8efebc6c138c8f75a1 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 4 Aug 2009 08:13:24 +0000 Subject: [PATCH] * samtools-0.1.5-24 (r435) * fixed a typo --- bamtk.c | 2 +- misc/samtools.pl | 93 ++++++++++++++++++++++++++++++++++++++++++------ sam_view.c | 2 +- 3 files changed, 84 insertions(+), 13 deletions(-) diff --git a/bamtk.c b/bamtk.c index 7c6b5ff..0b41561 100644 --- a/bamtk.c +++ b/bamtk.c @@ -9,7 +9,7 @@ #endif #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.5-23 (r434)" +#define PACKAGE_VERSION "0.1.5-24 (r435)" #endif int bam_taf2baf(int argc, char *argv[]); diff --git a/misc/samtools.pl b/misc/samtools.pl index ade5289..c175539 100755 --- a/misc/samtools.pl +++ b/misc/samtools.pl @@ -10,7 +10,8 @@ my $version = '0.3.2 (r321)'; &usage if (@ARGV < 1); my $command = shift(@ARGV); -my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, unique=>\&unique); +my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, + unique=>\&unique, uniqcmp=>\&uniqcmp); die("Unknown command \"$command\".\n") if (!defined($func{$command})); &{$func{$command}}; @@ -27,7 +28,7 @@ sub showALEN { next if (/^\@/ || @t < 11); my $l = 0; $_ = $t[5]; - s/(\d+)[SMI]/$l+=$1/eg; + s/(\d+)[MI]/$l+=$1/eg; print join("\t", @t[0..5]), "\t$l\t", join("\t", @t[6..$#t]), "\n"; } } @@ -220,10 +221,11 @@ sub p2q_print_str { # sub unique { - my %opts = (f=>5.0, q=>5, r=>2, a=>1, b=>3); - getopts('f:', \%opts); + my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3); + getopts('Qf:q:r:a:b:', \%opts); die("Usage: samtools.pl unique [-f $opts{f}] \n") if (@ARGV == 0 && -t STDIN); my $last = ''; + my $recal_Q = !defined($opts{Q}); my @a; while (<>) { my $score = -1; @@ -239,19 +241,19 @@ sub unique { $cigar =~ s/(\d+)M/$mm+=$1/eg; $score = $mm * $opts{a} - $go * $opts{q} - $ge * $opts{r}; # no mismatches... } - $score = 0 if ($score < 0); + $score = 1 if ($score < 1); if ($t[0] ne $last) { - &unique_aux(\@a, $opts{f}) if (@a); + &unique_aux(\@a, $opts{f}, $recal_Q) if (@a); $last = $t[0]; } push(@a, [$score, \@t]); } - &unique_aux(\@a, $opts{f}) if (@a); + &unique_aux(\@a, $opts{f}, $recal_Q) if (@a); } sub unique_aux { - my ($a, $fac) = @_; - my ($max, $max2, $max_i) = (-1, -1, -1); + my ($a, $fac, $is_recal) = @_; + my ($max, $max2, $max_i) = (0, 0, -1); for (my $i = 0; $i < @$a; ++$i) { if ($a->[$i][0] > $max) { $max2 = $max; $max = $a->[$i][0]; $max_i = $i; @@ -259,12 +261,81 @@ sub unique_aux { $max2 = $a->[$i][0]; } } - my $q = int($fac * ($max - $max2) + .499); - $a->[$max_i][1][4] = $q < 250? $q : 250; + if ($is_recal) { + my $q = int($fac * ($max - $max2) / $max + .499); + $q = 250 if ($q > 250); + $a->[$max_i][1][4] = $q < 250? $q : 250; + } print join("\t", @{$a->[$max_i][1]}); @$a = (); } +# +# uniqcmp: compare two SAM files +# + +sub uniqcmp { + my %opts = (q=>10, s=>100); + getopts('pq:s:', \%opts); + die("Usage: samtools.pl uniqcmp \n") if (@ARGV < 2); + my ($fh, %a); + warn("[uniqcmp] read the first file...\n"); + &uniqcmp_aux($ARGV[0], \%a, 0); + warn("[uniqcmp] read the second file...\n"); + &uniqcmp_aux($ARGV[1], \%a, 1); + warn("[uniqcmp] stats...\n"); + my @cnt; + $cnt[$_] = 0 for (0..9); + for my $x (keys %a) { + my $p = $a{$x}; + my $z; + if (defined($p->[0]) && defined($p->[1])) { + $z = ($p->[0][0] == $p->[1][0] && $p->[0][1] eq $p->[1][1] && abs($p->[0][2] - $p->[1][2]) < $opts{s})? 0 : 1; + if ($p->[0][3] >= $opts{q} && $p->[1][3] >= $opts{q}) { + ++$cnt[$z*3+0]; + } elsif ($p->[0][3] >= $opts{q}) { + ++$cnt[$z*3+1]; + } elsif ($p->[1][3] >= $opts{q}) { + ++$cnt[$z*3+2]; + } + print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t", + $p->[0][5]-$p->[1][5], "\n" if ($z && defined($opts{p}) && ($p->[0][3] >= $opts{q} || $p->[1][3] >= $opts{q})); + } elsif (defined($p->[0])) { + ++$cnt[$p->[0][3]>=$opts{q}? 6 : 7]; + } else { + ++$cnt[$p->[1][3]>=$opts{q}? 8 : 9]; + } + } + print "Consistent (high, high): $cnt[0]\n"; + print "Consistent (high, low ): $cnt[1]\n"; + print "Consistent (low , high): $cnt[2]\n"; + print "Inconsistent (high, high): $cnt[3]\n"; + print "Inconsistent (high, low ): $cnt[4]\n"; + print "Inconsistent (low , high): $cnt[5]\n"; + print "Second missing (high): $cnt[6]\n"; + print "Second missing (low ): $cnt[7]\n"; + print "First missing (high): $cnt[8]\n"; + print "First missing (low ): $cnt[9]\n"; +} + +sub uniqcmp_aux { + my ($fn, $a, $which) = @_; + my $fh; + $fn = "samtools view $fn |" if ($fn =~ /\.bam/); + open($fh, $fn) || die; + while (<$fh>) { + my @t = split; + next if (@t < 11); + my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0; + my ($x, $nm) = (0, 0); + $nm = $1 if (/NM:i:(\d+)/); + $_ = $t[5]; + s/(\d+)[MI]/$x+=$1/eg; + @{$a->{$t[0]}[$which]} = (($t[1]&0x10)? 1 : 0, $t[2], $t[3]-$l, $t[4], "$x:$nm", $x - 4 * $nm); + } + close($fh); +} + # # Usage # diff --git a/sam_view.c b/sam_view.c index 2e89921..113c6c4 100644 --- a/sam_view.c +++ b/sam_view.c @@ -140,7 +140,7 @@ static int usage(int is_long_help) fprintf(stderr, " -S input is SAM\n"); fprintf(stderr, " -u uncompressed BAM output (force -b)\n"); fprintf(stderr, " -x output FLAG in HEX (samtools-C specific)\n"); - fprintf(stderr, " -X output FLAG in stirng (samtools-C specific)\n"); + fprintf(stderr, " -X output FLAG in string (samtools-C specific)\n"); fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n"); fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n"); fprintf(stderr, " -o FILE output file name [stdout]\n"); -- 2.39.2